Search Results for "linux command" - Page 5
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Showing 129 open source projects for "linux command"
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The TandemSearcher is a Java based application for searching for tandem repeats in the DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).
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PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.
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MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system
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The ExactFDR software package is an improvement of permutation-based False Discovery Rate (FDR) estimation methods that takes advantage from exact p-value computations for analyzing Genome-wide association studies data
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Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
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The YeastsIdentification is a Java based application for searching for unique DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).
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A platform for the integration of deterministic and stochastic models, for the simulation of the integrated models and for interactive exploration of the model behaviour.
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The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
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Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.
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The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.
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Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.
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OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses.
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The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.
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Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
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In order to facilitate standardization and exchange of microarray layout, this project provides an ADF (Array design File))/MAGE-ML converter.
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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
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neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
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A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
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Yawn: Yet Another W* Network: a java framework for developing, training and testing neural networks independently of the model and test environment.
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NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
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A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed source code (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste
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